PXD011330 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Assessing Technical and Biological Variation in SWATH-MS -based Proteomics: A case study in Chronic Lymphocytic Leukaemia |
Description | Chronic lymphocytic leukaemia (CLL) is renowned for its variable clinical course and response to therapy, suggesting a role for precision medicine. However, the molecular basis of CLL variability remains incompletely understood. Recent developments in data independent acquisition (DIA) -MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. This report describes the sample replication and data handling requirements for SWATH-MS analysis of clinical samples. A CLL-specific spectral library compromising over 1,500,000 spectra with digital information for over 150,000 peptides has been generated to enable the quantification of up to 7736 proteins. To assess the reproducibility of the assay, SWATH-MS analysis was performed on 6 cryopreserved CLL patient samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins (<1% FDR) across 54 SWATH-MS acquisitions. These analyses showed that SWATH-MS is a highly reproducible technique. However, replicate sample preparations on different days was identified as the main source of variation. To overcome the effect of variation between sample preparation batches, different computational approaches for batch correction were tested. All approaches successfully removed technical variability whilst retaining proteomic differences between clinical subgroups. Functional enrichment analysis of proteins associated to IGHV mutational status highlighted the importance of metabolic remodelling in the biology of CLL and overlapped significantly with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was developed. This approach could be used to drive the design of future CLL SWATH-MS studies. These fundamental requirements for DIA approaches should be widely applicable to other clinical proteomics studies. |
HostingRepository | PRIDE |
AnnounceDate | 2021-02-05 |
AnnouncementXML | Submission_2021-02-05_06:47:34.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Gina Eagle |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | TripleTOF 6600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-10-10 05:38:39 | ID requested | |
⏵ 1 | 2021-02-05 06:47:34 | announced | |
2 | 2023-11-14 08:49:48 | announced | 2023-11-14: Updated project metadata. |
Publication List
Keyword List
curator keyword: Biomedical |
submitter keyword: CLL, SWATH, Leukaemia |
Contact List
Dr Rosalind Jenkins |
contact affiliation | MRC Centre for Drug Safety Science, Dept. Molecular & Clinical Pharmacology, Institute for Translational Medicine, University of Liverpool, UK. |
contact email | R.Jenkins@liv.ac.uk |
lab head | |
Gina Eagle |
contact affiliation | University of Liverpool |
contact email | gleagle@liverpool.ac.uk |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/02/PXD011330 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD011330
- Label: PRIDE project
- Name: Assessing Technical and Biological Variation in SWATH-MS -based Proteomics: A case study in Chronic Lymphocytic Leukaemia